motifmatchr 1.2.0
Alicia Schep
| Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018) |
| URL: https://git.bioconductor.org/packages/motifmatchr |
| Branch: RELEASE_3_7 |
| Last Commit: 032b47a |
| Last Changed Date: 2018-04-30 10:35:47 -0400 (Mon, 30 Apr 2018) |
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | OK | |  |
| tokay2 | Windows Server 2012 R2 Standard / x64 | [ OK ] | OK | WARNINGS | OK | |
| merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
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### Running command:
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### C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.7/bioc/src/contrib/motifmatchr_1.2.0.tar.gz && rm -rf motifmatchr.buildbin-libdir && mkdir motifmatchr.buildbin-libdir && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=motifmatchr.buildbin-libdir motifmatchr_1.2.0.tar.gz && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL motifmatchr_1.2.0.zip && rm motifmatchr_1.2.0.tar.gz motifmatchr_1.2.0.zip
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% Total % Received % Xferd Average Speed Time Time Time Current
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100 77989 100 77989 0 0 1500k 0 --:--:-- --:--:-- --:--:-- 1730k
install for i386
* installing *source* package 'motifmatchr' ...
** libs
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I. -I./MOODS/ -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/RcppArmadillo/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c RcppExports.cpp -o RcppExports.o
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I. -I./MOODS/ -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/RcppArmadillo/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c r_interface.cpp -o r_interface.o
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I. -I./MOODS/ -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/RcppArmadillo/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c MOODS/scanner.cpp -o MOODS/scanner.o
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I. -I./MOODS/ -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/RcppArmadillo/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c MOODS/motif_h.cpp -o MOODS/motif_h.o
MOODS/motif_h.cpp: In member function 'std::vector<double> MOODS::scan::MotifH::expected_scores(const std::vector<double>&)':
MOODS/motif_h.cpp:26:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (int i = 0; i < cols; ++i){
^
MOODS/motif_h.cpp:27:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (int j = 0; j < rows; ++j){
^
MOODS/motif_h.cpp: In member function 'virtual std::pair<bool, double> MOODS::scan::MotifH::check_hit(const string&, const std::vector<unsigned char>&, std::size_t, double)':
MOODS/motif_h.cpp:256:25: warning: suggest parentheses around arithmetic in operand of '^' [-Wparentheses]
CODE = MASK & (CODE << SHIFT) ^ alphabet_map[s[ii + i + q - 1]];
^
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I. -I./MOODS/ -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/RcppArmadillo/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c MOODS/motif_0.cpp -o MOODS/motif_0.o
MOODS/motif_0.cpp: In function 'std::vector<double> MOODS::scan::expected_differences(const score_matrix&, const std::vector<double>&)':
MOODS/motif_0.cpp:28:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (int i = 0; i < m; ++i)
^
MOODS/motif_0.cpp:31:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (int j = 0; j < a; ++j)
^
MOODS/motif_0.cpp:38:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (int j = 0; j < a; ++j)
^
MOODS/motif_0.cpp: In function 'unsigned int MOODS::scan::window_position(const std::vector<double>&, unsigned int, unsigned int)':
MOODS/motif_0.cpp:64:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (int i = 0; i < m - l; ++i)
^
MOODS/motif_0.cpp: In function 'std::vector<unsigned int> MOODS::scan::compute_lookahead_order(const std::vector<double>&, unsigned int, unsigned int, unsigned int)':
MOODS/motif_0.cpp:96:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (int i = 0; i < window_pos; ++i)
^
MOODS/motif_0.cpp:100:38: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (int i = window_pos+l; i < m; ++i)
^
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I. -I./MOODS/ -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/RcppArmadillo/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c MOODS/moods_tools.cpp -o MOODS/moods_tools.o
MOODS/moods_tools.cpp: In function 'double MOODS::tools::threshold_from_p(const score_matrix&, const std::vector<double>&, const double&)':
MOODS/moods_tools.cpp:155:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (size_t i = 0; i < n; ++i)
^
MOODS/moods_tools.cpp:157:30: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (size_t j = 0; j < a; ++j)
^
MOODS/moods_tools.cpp:168:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (size_t i = 0; i < n; ++i)
^
MOODS/moods_tools.cpp:172:30: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (size_t j = 1; j < a; ++j)
^
MOODS/moods_tools.cpp:190:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (size_t j = 0; j < a; ++j)
^
MOODS/moods_tools.cpp:193:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (size_t i = 1; i < n; ++i)
^
MOODS/moods_tools.cpp:195:30: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (size_t j = 0; j < a; ++j)
^
MOODS/moods_tools.cpp: In function 'score_matrix MOODS::tools::log_odds(const std::vector<std::vector<double> >&, const std::vector<std::vector<double> >&, const std::vector<double>&, double, std::size_t)':
MOODS/moods_tools.cpp:320:38: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (size_t PCODE = 0; PCODE < 1 << (SHIFT * r); ++PCODE ){
^
MOODS/moods_tools.cpp:328:46: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (size_t SCODE = 0; SCODE < 1 << (SHIFT * (q - r - 1)); ++SCODE){
^
MOODS/moods_tools.cpp: In function 'double MOODS::tools::threshold_from_p(const score_matrix&, const std::vector<double>&, const double&, std::size_t)':
MOODS/moods_tools.cpp:454:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (size_t i = 0; i < cols; ++i)
^
MOODS/moods_tools.cpp:456:36: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (size_t CODE = 0; CODE < rows; ++CODE)
^
MOODS/moods_tools.cpp:468:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (size_t i = 0; i < cols; ++i)
^
MOODS/moods_tools.cpp:472:36: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (size_t CODE = 1; CODE < rows; ++CODE)
^
MOODS/moods_tools.cpp:489:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (size_t CODE = 0; CODE < (1 << (SHIFT * q)); ++CODE){
^
MOODS/moods_tools.cpp:500:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (size_t i = 1; i < cols; ++i)
^
MOODS/moods_tools.cpp:503:36: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (size_t CODE = 0; CODE < (1 << (SHIFT * q)); ++CODE)
^
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I. -I./MOODS/ -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/RcppArmadillo/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c MOODS/moods_scan.cpp -o MOODS/moods_scan.o
MOODS/moods_scan.cpp: In function 'std::vector<std::vector<MOODS::match> > MOODS::scan::scan_best_hits_dna(const string&, const std::vector<std::vector<std::vector<double> > >&, std::size_t, int, unsigned int, std::size_t, std::size_t)':
MOODS/moods_scan.cpp:97:14: warning: unused variable 'done' [-Wunused-variable]
bool done = 0;
^
MOODS/moods_scan.cpp: In function 'std::vector<MOODS::match> MOODS::scan::naive_scan_dna(const string&, score_matrix, double, std::size_t)':
MOODS/moods_scan.cpp:252:33: warning: suggest parentheses around arithmetic in operand of '|' [-Wparentheses]
CODE = MASK & (CODE << SHIFT) | alphabet_map[seq[i+j+q-1]];
^
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I. -I./MOODS/ -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/RcppArmadillo/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c MOODS/moods_parsers.cpp -o MOODS/moods_parsers.o
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I. -I./MOODS/ -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/RcppArmadillo/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c MOODS/moods_misc.cpp -o MOODS/moods_misc.o
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I. -I./MOODS/ -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/RcppArmadillo/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c MOODS/match_types.cpp -o MOODS/match_types.o
C:/Rtools/mingw_32/bin/g++ -shared -s -static-libgcc -o motifmatchr.dll tmp.def ./RcppExports.o ./r_interface.o ./MOODS/scanner.o ./MOODS/motif_h.o ./MOODS/motif_0.o ./MOODS/moods_tools.o ./MOODS/moods_scan.o ./MOODS/moods_parsers.o ./MOODS/moods_misc.o ./MOODS/match_types.o -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.7-bioc/meat/motifmatchr.buildbin-libdir/motifmatchr/libs/i386
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'motifmatchr'
finding HTML links ... done
example_motifs html
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp8U5nJc/R.INSTALL1d0c61d475c5/motifmatchr/man/example_motifs.Rd:11: file link 'PFMatrixList' in package 'TFBSTools' does not exist and so has been treated as a topic
matchMotifs html
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp8U5nJc/R.INSTALL1d0c61d475c5/motifmatchr/man/matchMotifs.Rd:52: file link 'PFMatrix' in package 'TFBSTools' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp8U5nJc/R.INSTALL1d0c61d475c5/motifmatchr/man/matchMotifs.Rd:53: file link 'PFMatrixList' in package 'TFBSTools' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp8U5nJc/R.INSTALL1d0c61d475c5/motifmatchr/man/matchMotifs.Rd:53: file link 'PWMatrix' in package 'TFBSTools' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp8U5nJc/R.INSTALL1d0c61d475c5/motifmatchr/man/matchMotifs.Rd:54: file link 'PWMatrixList' in package 'TFBSTools' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp8U5nJc/R.INSTALL1d0c61d475c5/motifmatchr/man/matchMotifs.Rd:56: file link 'GenomicRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp8U5nJc/R.INSTALL1d0c61d475c5/motifmatchr/man/matchMotifs.Rd:57: file link 'DNAStringSet' in package 'Biostrings' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp8U5nJc/R.INSTALL1d0c61d475c5/motifmatchr/man/matchMotifs.Rd:57: file link 'DNAString' in package 'Biostrings' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp8U5nJc/R.INSTALL1d0c61d475c5/motifmatchr/man/matchMotifs.Rd:62: file link 'DNAStringSet' in package 'Biostrings' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp8U5nJc/R.INSTALL1d0c61d475c5/motifmatchr/man/matchMotifs.Rd:63: file link 'FaFile' in package 'Rsamtools' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp8U5nJc/R.INSTALL1d0c61d475c5/motifmatchr/man/matchMotifs.Rd:64: file link 'getBSgenome' in package 'BSgenome' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp8U5nJc/R.INSTALL1d0c61d475c5/motifmatchr/man/matchMotifs.Rd:65: file link 'GenomicRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp8U5nJc/R.INSTALL1d0c61d475c5/motifmatchr/man/matchMotifs.Rd:66: file link 'RangedSummarizedExperiment' in package 'SummarizedExperiment' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp8U5nJc/R.INSTALL1d0c61d475c5/motifmatchr/man/matchMotifs.Rd:89: file link 'GenomicRangesList' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp8U5nJc/R.INSTALL1d0c61d475c5/motifmatchr/man/matchMotifs.Rd:90: file link 'IRangesList' in package 'IRanges' does not exist and so has been treated as a topic
motifCounts html
motifMatches html
motifScores html
motifmatchr html
motifmatchr_deprecated html
pwmType html
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL
install for x64
* installing *source* package 'motifmatchr' ...
** libs
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I. -I./MOODS/ -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/RcppArmadillo/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c RcppExports.cpp -o RcppExports.o
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I. -I./MOODS/ -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/RcppArmadillo/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c r_interface.cpp -o r_interface.o
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I. -I./MOODS/ -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/RcppArmadillo/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c MOODS/scanner.cpp -o MOODS/scanner.o
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I. -I./MOODS/ -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/RcppArmadillo/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c MOODS/motif_h.cpp -o MOODS/motif_h.o
MOODS/motif_h.cpp: In member function 'std::vector<double> MOODS::scan::MotifH::expected_scores(const std::vector<double>&)':
MOODS/motif_h.cpp:26:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (int i = 0; i < cols; ++i){
^
MOODS/motif_h.cpp:27:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (int j = 0; j < rows; ++j){
^
MOODS/motif_h.cpp: In member function 'virtual std::pair<bool, double> MOODS::scan::MotifH::check_hit(const string&, const std::vector<unsigned char>&, std::size_t, double)':
MOODS/motif_h.cpp:256:25: warning: suggest parentheses around arithmetic in operand of '^' [-Wparentheses]
CODE = MASK & (CODE << SHIFT) ^ alphabet_map[s[ii + i + q - 1]];
^
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I. -I./MOODS/ -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/RcppArmadillo/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c MOODS/motif_0.cpp -o MOODS/motif_0.o
MOODS/motif_0.cpp: In function 'std::vector<double> MOODS::scan::expected_differences(const score_matrix&, const std::vector<double>&)':
MOODS/motif_0.cpp:28:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (int i = 0; i < m; ++i)
^
MOODS/motif_0.cpp:31:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (int j = 0; j < a; ++j)
^
MOODS/motif_0.cpp:38:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (int j = 0; j < a; ++j)
^
MOODS/motif_0.cpp: In function 'unsigned int MOODS::scan::window_position(const std::vector<double>&, unsigned int, unsigned int)':
MOODS/motif_0.cpp:64:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (int i = 0; i < m - l; ++i)
^
MOODS/motif_0.cpp: In function 'std::vector<unsigned int> MOODS::scan::compute_lookahead_order(const std::vector<double>&, unsigned int, unsigned int, unsigned int)':
MOODS/motif_0.cpp:96:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (int i = 0; i < window_pos; ++i)
^
MOODS/motif_0.cpp:100:38: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (int i = window_pos+l; i < m; ++i)
^
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I. -I./MOODS/ -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/RcppArmadillo/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c MOODS/moods_tools.cpp -o MOODS/moods_tools.o
MOODS/moods_tools.cpp: In function 'double MOODS::tools::threshold_from_p(const score_matrix&, const std::vector<double>&, const double&)':
MOODS/moods_tools.cpp:155:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (size_t i = 0; i < n; ++i)
^
MOODS/moods_tools.cpp:157:30: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (size_t j = 0; j < a; ++j)
^
MOODS/moods_tools.cpp:168:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (size_t i = 0; i < n; ++i)
^
MOODS/moods_tools.cpp:172:30: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (size_t j = 1; j < a; ++j)
^
MOODS/moods_tools.cpp:190:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (size_t j = 0; j < a; ++j)
^
MOODS/moods_tools.cpp:193:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (size_t i = 1; i < n; ++i)
^
MOODS/moods_tools.cpp:195:30: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (size_t j = 0; j < a; ++j)
^
MOODS/moods_tools.cpp: In function 'score_matrix MOODS::tools::log_odds(const std::vector<std::vector<double> >&, const std::vector<std::vector<double> >&, const std::vector<double>&, double, std::size_t)':
MOODS/moods_tools.cpp:320:38: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (size_t PCODE = 0; PCODE < 1 << (SHIFT * r); ++PCODE ){
^
MOODS/moods_tools.cpp:328:46: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (size_t SCODE = 0; SCODE < 1 << (SHIFT * (q - r - 1)); ++SCODE){
^
MOODS/moods_tools.cpp: In function 'double MOODS::tools::threshold_from_p(const score_matrix&, const std::vector<double>&, const double&, std::size_t)':
MOODS/moods_tools.cpp:454:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (size_t i = 0; i < cols; ++i)
^
MOODS/moods_tools.cpp:456:36: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (size_t CODE = 0; CODE < rows; ++CODE)
^
MOODS/moods_tools.cpp:468:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (size_t i = 0; i < cols; ++i)
^
MOODS/moods_tools.cpp:472:36: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (size_t CODE = 1; CODE < rows; ++CODE)
^
MOODS/moods_tools.cpp:489:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (size_t CODE = 0; CODE < (1 << (SHIFT * q)); ++CODE){
^
MOODS/moods_tools.cpp:500:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (size_t i = 1; i < cols; ++i)
^
MOODS/moods_tools.cpp:503:36: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (size_t CODE = 0; CODE < (1 << (SHIFT * q)); ++CODE)
^
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I. -I./MOODS/ -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/RcppArmadillo/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c MOODS/moods_scan.cpp -o MOODS/moods_scan.o
MOODS/moods_scan.cpp: In function 'std::vector<std::vector<MOODS::match> > MOODS::scan::scan_best_hits_dna(const string&, const std::vector<std::vector<std::vector<double> > >&, std::size_t, int, unsigned int, std::size_t, std::size_t)':
MOODS/moods_scan.cpp:97:14: warning: unused variable 'done' [-Wunused-variable]
bool done = 0;
^
MOODS/moods_scan.cpp: In function 'std::vector<MOODS::match> MOODS::scan::naive_scan_dna(const string&, score_matrix, double, std::size_t)':
MOODS/moods_scan.cpp:252:33: warning: suggest parentheses around arithmetic in operand of '|' [-Wparentheses]
CODE = MASK & (CODE << SHIFT) | alphabet_map[seq[i+j+q-1]];
^
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I. -I./MOODS/ -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/RcppArmadillo/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c MOODS/moods_parsers.cpp -o MOODS/moods_parsers.o
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I. -I./MOODS/ -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/RcppArmadillo/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c MOODS/moods_misc.cpp -o MOODS/moods_misc.o
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I. -I./MOODS/ -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/RcppArmadillo/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c MOODS/match_types.cpp -o MOODS/match_types.o
C:/Rtools/mingw_64/bin/g++ -shared -s -static-libgcc -o motifmatchr.dll tmp.def ./RcppExports.o ./r_interface.o ./MOODS/scanner.o ./MOODS/motif_h.o ./MOODS/motif_0.o ./MOODS/moods_tools.o ./MOODS/moods_scan.o ./MOODS/moods_parsers.o ./MOODS/moods_misc.o ./MOODS/match_types.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.7-bioc/meat/motifmatchr.buildbin-libdir/motifmatchr/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'motifmatchr' as motifmatchr_1.2.0.zip
* DONE (motifmatchr)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.7-bioc/R/library'
package 'motifmatchr' successfully unpacked and MD5 sums checked
In R CMD INSTALL